Update environment.yml

[curtcorum]

#399 (comment)

Adding https://github.com/yuvipanda/jupyter-pluto-proxy so that Pluto can be used from JupyterLab in binder instances.

Pluto should only get loaded in the docker instance, if I understand correctly.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 89.00%. Comparing base (7f4ecdf) to head (e591a37).

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  Files          44       44           
  Lines        2746     2746           
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[cncastillo]

Looks great! Fingers crossed this works 🤞.

[cncastillo]

I will try to generate a docker image of this PR with MyBinder. If that is not possible I will just merge to test it.

[cncastillo]

I was able to create an image! https://mybinder.org/v2/gh/curtcorum/KomaMRI.jl/docker_jupyterlab_pluto

But I could not launch the Pluto server, probably we still need to add Pluto.jl in the Dockerfile, like in https://github.com/yuvipanda/jupyter-pluto-proxy/blob/main/Dockerfile#L10.

[curtcorum]

Great, and not great! There is no doubt some configuration for docker, and potentially for the jupyter-pluto-proxy file config to get spefic notebooks to spin up. I spent a bit of time getting a local docker instance going for testing.

On June 3, 2024 10:53:39 PM CDT, Carlos Castillo Passi ***@***.***> wrote: I was able to create an image! https://mybinder.org/v2/gh/curtcorum/KomaMRI.jl/docker_jupyterlab_pluto But I could not launch the Pluto server, probably we still need to add `Pluto.jl` in the `Dockerfile`, like in https://github.com/yuvipanda/jupyter-pluto-proxy/blob/main/Dockerfile#L10. -- Reply to this email directly or view it on GitHub: #400 (comment) You are receiving this because you authored the thread. Message ID: ***@***.***>

-- Sent from my Android device with K-9 Mail. Please excuse my brevity.

[cncastillo]

It works! if I install Pluto, PlutoUI and PlutoPlotly using JupyterLab's Julia console, I can run Pluto notebooks!

To take advantage of Binder's prebuilt environment, I had to disable the reproducible aspect of the Pluto notebook using

begin
    import Pkg
    Pkg.activate("/home/jovyan/") # Use prebuilt environment (with Koma preinstalled)
end

I think it is worth sacrificing reproducibility (Pluto's internal Manifest.toml info), to make the experience better for the user (the code runs faster).

[curtcorum]

Awesome!

On June 3, 2024 11:26:44 PM CDT, Carlos Castillo Passi ***@***.***> wrote: It works! if I install `Pluto`, `PlutoUI` and `PlutoPlotly` using JupyterLab's Julia console, I can run Pluto notebooks quite fast!  To take advantage of Binder's prebuilt environment, I disabled the reproducible aspect of the Pluto notebook with ```julia begin import Pkg Pkg.activate("/home/jovyan/") # Use environment with Koma preinstalled end ``` -- Reply to this email directly or view it on GitHub: #400 (comment) You are receiving this because you authored the thread. Message ID: ***@***.***>

-- Sent from my Android device with K-9 Mail. Please excuse my brevity.

[curtcorum]

@cncastillo

Update, we can launch a specific Jupyter notebook (python or julia) from a binder link, also can launch into an active Pluto start page session...still cannot go direct to a specific Pluto notebook...

see: #399 (comment)

[cncastillo]

Amazing, when this is merged, we can point to the gh-pages branch with all the generated notebooks. Literate already offers a variable @__BINDER_ROOT_URL__ that could be useful for this (example: https://fredrikekre.github.io/Literate.jl/v2/generated/example/). I am testing it on #403.

[cncastillo]

Ok, the links to the binder work properly with Literate, but the docker image fails to generate (https://mybinder.org/v2/gh/JuliaHealth/KomaMRI.jl/gh-pages). I will need to take a look later this week.

[cncastillo]

Hi! I managed to fix this in dev! No extra dependency was added to KomaMRI, and no postBuild script was needed (everything is in .binder/).

https://juliahealth.org/KomaMRI.jl/dev/

• Literate tutorial: https://mybinder.org/v2/gh/JuliaHealth/KomaMRI.jl/master?urlpath=git-pull%3Frepo%3Dhttps%253A%252F%252Fgithub.com%252FJuliaHealth%252FKomaMRI.jl%26urlpath%3Dlab%252Ftree%252FKomaMRI.jl%252Fdev%252Ftutorial%252F01-FID.ipynb%26branch%3Dgh-pages
• Pluto tutorial: https://mybinder.org/v2/gh/JuliaHealth/KomaMRI.jl/master?urlpath=git-pull%3Frepo%3Dhttps%253A%252F%252Fgithub.com%252FJuliaHealth%252FKomaMRI.jl%26urlpath%3Dpluto%252Fopen%3Fpath%3DKomaMRI.jl%252Fdev%252Ftutorial-pluto%252F01-gradient-echo-spin-echo.jl%26branch%3Dgh-pages

Sometimes, building the docker image times out, but that will be fixed when we tag v0.9, which removes CUDA as a strong dependency.

Also, I am not completely sure how to make Pluto notebooks use the compiled environment by default yet, but at least they work and open directly!

EDIT: modifying the package loading cell to

begin
	import Pkg
	Pkg.activate("/home/jovyan/.binder/")
	using KomaMRI, PlutoPlotly, PlutoUI
end

seems to work.